X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhelp.jhm;h=3a4aac49effd972b15bd47113974d25d2ea736bf;hb=dcd8d3212242ef3bde7ff9d865f9dfb859407a30;hp=9eda49137ddaef79fef4f2845cc332eea7d0c289;hpb=8ee7a0f79f6da26d5011c60a80226d6994733cab;p=jalview.git

diff --git a/help/help.jhm b/help/help.jhm
index 9eda491..3a4aac4 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -10,15 +10,15 @@
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
    
    <mapID target="webservice" url="html/webServices/index.html"/>
-   <mapID target="clustal" url="html/webServices/msaws.html#clustal"/>
-   <mapID target="muscle" url="html/webServices/msaws.html#muscle"/>
+   <mapID target="clustal" url="html/webServices/clustal.html"/>
    
    <mapID target="io" url="html/io/index.html"/>
+   <mapID target="alformats" url="html/io/fileformats.html"/>
    <mapID target="edit" url="html/editing/index.html"/>
 
-   <mapID target="sorting" url="html/calculations/sorting.html"/>
+   <mapID target="calculations" url="html/calculations/index.html"/>
    <mapID target="trees" url="html/calculations/tree.html"/>
-   <mapID target="treeview" url="html/calculations/treeviewer.html"/>
+   <mapID target="sorting" url="html/calculations/sorting.html"/>
    <mapID target="pca" url="html/calculations/pca.html"/>
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>
    <mapID target="redundancy" url="html/calculations/redundancy.html"/>
@@ -39,6 +39,12 @@
    <mapID target="colours.abovepid" url="html/colourSchemes/abovePID.html"/>
    <mapID target="colours.conservation" url="html/colourSchemes/conservation.html"/>
    
+   <mapID target="menus" url="html/menus/index.html"/>
+   <mapID target="desktopMenu" url="html/menus/desktopMenu.html"/>
+   <mapID target="alMenu" url="html/menus/alignmentMenu.html"/>
+   <mapID target="popMenu" url="html/menus/popupMenu.html"/>
+   
+   
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />